changes to get rid of partial parts of input file paths

Author: alexandriai168

configuration/lc_fticr_enviroms.toml

@@ -6,8 +6,6 @@ time_block = 30 #seconds
 # Reference mass list:
 refmasslist_neg = "data/reference/Hawkes_neg.ref"
 # input output paths
-input_file_directory = "data/raw_data/..."
-input_file_name = "..."
 output_directory = "data/..."
 output_file_name = "..."
 output_file_type = ".csv"

enviroMS/LC_FTICR_workflow.py

@@ -32,8 +32,6 @@ class LC_FTICR_WorkflowParameters:
     refmasslist_neg: str = "data/referencec/Hawkes_neg.ref"
     # input output paths
     full_input_file_path: str = "data/raw_data/..."
-    input_file_directory: str = "data/raw_data/..."
-    input_file_name: str = "..."
     output_directory: str = "data/..."
     output_file_name: str = "..."
     output_file_type: str = ".csv"
@@ -338,8 +336,6 @@ def run_LC_FTICR_workflow_wdl(
     time_block,
     refmasslist_neg,
     full_input_file_path,
-    input_file_directory,
-    input_file_name,
     output_directory,
     output_file_name,
     output_file_type,
@@ -355,8 +351,6 @@ def run_LC_FTICR_workflow_wdl(
                                             time_block = time_block,
                                             refmasslist_neg = refmasslist_neg,
                                             full_input_file_path = full_input_file_path,
-                                            input_file_directory = input_file_directory,
-                                            input_file_name = input_file_name,
                                             output_directory = output_directory,
                                             output_file_name = output_file_name,
                                             output_file_type = output_file_type,

enviroMS/cli.py

@@ -170,8 +170,6 @@ def run_lc_fticr(lc_fticr_workflow_paramaters_file):
 @click.argument("end_time", required=True, type=float)
 @click.argument("time_block", required=True, type=float)
 @click.argument("refmasslist_neg", required=True, type=str)
-@click.argument("input_file_directory", required=True, type=str)
-@click.argument("input_file_name", required=True, type=str)
 @click.argument("output_directory", required=True, type=str)
 @click.argument("output_file_name", required=True, type=str)
 @click.argument("output_file_type", required=True, type=str)
@@ -186,8 +184,6 @@ def run_lc_fticr_wdl(
     end_time,
     time_block,
     refmasslist_neg,
-    input_file_directory,
-    input_file_name,
     output_directory,
     output_file_name,
     output_file_type,
@@ -205,8 +201,6 @@ def run_lc_fticr_wdl(
         end_time = end_time,
         time_block = time_block,
         refmasslist_neg = refmasslist_neg,
-        input_file_directory = input_file_directory,
-        input_file_name = input_file_name,
         output_directory = output_directory,
         output_file_name = output_file_name,
         output_file_type = output_file_type,

wdl/lc_fticr_ms.wdl

@@ -23,8 +23,6 @@ task run_LCFTICR {
         Float end_time
         Float time_block
         File refmasslist_neg
-        String input_file_directory
-        String input_file_name
         String output_directory
         String output_file_name
         String output_file_type
@@ -45,8 +43,6 @@ task run_LCFTICR {
             ${end_time} \
             ${time_block} \
             ${refmasslist_neg} \
-            ${input_file_directory} \
-            ${input_file_name} \
             ${output_directory} \
             ${output_file_name} \
             ${output_file_type} \

wdl/lc_fticr_wdl_input.json

@@ -6,8 +6,6 @@
     "lc_ft_icr_ms.run_LCFTICR.refmasslist_neg": "data/reference/Hawkes_neg.ref",
 
     "lc_ft_icr_ms.run_LCFTICR.full_input_file_path": ["./data/raw_data/lc_fticr/20231109_60885_SRFA_50ppm_5uL_LC_PolarAdv-001262_231109183242.raw"],
-    "lc_ft_icr_ms.run_LCFTICR.input_file_directory": "data/raw_data/lc_fticr/",
-    "lc_ft_icr_ms.run_LCFTICR.input_file_name": "20231109_60885_SRFA_50ppm_5uL_LC_PolarAdv-001262_231109183242.raw",
     "lc_ft_icr_ms.run_LCFTICR.output_directory": "data/",
     "lc_ft_icr_ms.run_LCFTICR.output_file_name": "lcfticr_test_output",
     "lc_ft_icr_ms.run_LCFTICR.output_file_type": "csv",

wdl/lc_fticr_wdl_input_local_docker.json

@@ -8,8 +8,6 @@
     "lc_ft_icr_ms.run_LCFTICR.refmasslist_neg": "./data/reference/Hawkes_neg.ref",
 
     "lc_ft_icr_ms.run_LCFTICR.full_input_file_path": ["./data/raw_data/lc_fticr/20231109_60885_SRFA_50ppm_5uL_LC_PolarAdv-001262_231109183242.raw"],
-    "lc_ft_icr_ms.run_LCFTICR.input_file_directory": "./data/raw_data/lc_fticr/",
-    "lc_ft_icr_ms.run_LCFTICR.input_file_name": "20231109_60885_SRFA_50ppm_5uL_LC_PolarAdv-001262_231109183242.raw",
     "lc_ft_icr_ms.run_LCFTICR.output_directory": "./data/",
     "lc_ft_icr_ms.run_LCFTICR.output_file_name": "lcfticr_test_output",
     "lc_ft_icr_ms.run_LCFTICR.output_file_type": "csv",